Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping

doi:10.3389/fpls.2022.921029

	Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping
	Wang, Lan 1,2; Liu, Yang 1,2; Zhao, Haiyan 3; Zheng, Yuebin 2,4; Bai, Feng 1,2; Deng, Sicheng ; Chen, Zhixiong 1,2; Wu, Jinwen 1,2; Liu, Xiangdong 1,2
	2022
发表期刊	FRONTIERS IN PLANT SCIENCE
ISSN	1664-462X
卷号	13
摘要	Grain length (GL) directly affects the yield and quality of rice. Very few cloned GL-related genes are applied in production because their yield-increasing effects are not obvious, and the overall regulatory networks underlying the associated processes remain poorly understood. DNA samples from two bulk DNA pools (L-pool and S-pool) and their parents (KJ01 and Huaye 3) were subjected to high-throughput sequencing. Using bulked segregant analysis (BSA), qGL3.5 was mapped to a 0.34-Mb hotspot region on chromosome 3 that contains 37 genes related to various traits. Then, qGL3.5 was mapped to the genomic interval between the flanking markers M2 and M3 using 2786 BC4F2 individuals. Because the region from B5 to B6 was not the associated region under BSA-seq analysis, qGL3.5 was narrowed down to the interval between B6 and M3, which spanned 24.0-kb. Of all 37 genes with non-synonymous single-nucleotide polymorphisms (SNPs) between KJ01 and Huaye 3 based on BSA-seq analysis, only one complete annotated gene, ORF18 (Gene ID: LOC_Os03g42790.1) was found. ORF18 encodes an IBR-RING zinc-finger-related protein, with one really interesting new gene (RING) and two in between ring finger (IBR) domains. The knockout of ORF18 derived from Huaye 3 using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) editing technology increased the GL of the mutant by approximately 2.2 mm. The novel locus qGL3.5 negatively regulated GL by promoting elongation of the longitudinal cell of the grain outer glume. These results provide a new genetic resource for rice grain shape breeding and a starting point for the functional characterization of the wild rice GL gene.
关键词	wild rice grain length BSA fine mapping gene cloning
学科领域	Plant Sciences
DOI	10.3389/fpls.2022.921029
收录类别	SCI
语种	英语
WOS关键词	QUANTITATIVE TRAIT LOCI ; GENETIC-ANALYSIS ; SIZE ; NUMBER ; YIELD ; SEQ ; DNA
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000817988900001
出版者	FRONTIERS MEDIA SA
文献子类	Article
出版地	LAUSANNE
资助机构	Laboratory of Lingnan Modern Agriculture Project [NT2021001] ; Guangdong Provincial Natural Science Foundation Program [2019A1515011826] ; Guangdong Provincial Special Projects in Key Field of Rural Revitalization [2020ZDZX1038] ; University Students' Innovation Project of South China Agricultural University [S202010564128]
作者邮箱	xdliu@scau.edu.cn
作品OA属性	gold, Green Published
引用统计	被引频次：5[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/28883
专题	植被与环境变化国家重点实验室
作者单位	1.South China Agr Univ, State Key Lab Conservat & Utilizat Subtrop Agrobio, Guangzhou, Peoples R China 2.Guangdong Lab Lingnan Modern Agr, Guangzhou, Peoples R China 3.South China Agr Univ, Coll Agr, Guangdong Prov Key Lab Plant Mol Breeding, Guangzhou, Peoples R China 4.Songgang Middle Sch, Qingyuan, Peoples R China 5.Chinese Acad Sci, Inst Bot, State Key Lab Vegetat & Environm Change, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Wang, Lan,Liu, Yang,Zhao, Haiyan,et al. Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping[J]. FRONTIERS IN PLANT SCIENCE,2022,13.
APA	Wang, Lan.,Liu, Yang.,Zhao, Haiyan.,Zheng, Yuebin.,Bai, Feng.,...&Liu, Xiangdong.(2022).Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping.FRONTIERS IN PLANT SCIENCE,13.
MLA	Wang, Lan,et al."Identification of qGL3.5, a Novel Locus Controlling Grain Length in Rice Through Bulked Segregant Analysis and Fine Mapping".FRONTIERS IN PLANT SCIENCE 13(2022).

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